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Hu X, Jiang L, Liu X, Chang H, Dong H, Yan J, Zhou X, Kong M. The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections. Microbiol Spectr 2024:e0045824. [PMID: 38916357 DOI: 10.1128/spectrum.00458-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
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Affiliation(s)
- Xiaohang Hu
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Liqing Jiang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaowei Liu
- Department of Intensive Care Unit, Affiliated Hospital of Jining Medical University,Jining Medical University, Shandong Jining, China
| | - Hong Chang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Haixin Dong
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Jinyan Yan
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaoya Zhou
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Min Kong
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
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Wang Q, Chen Y, Chen Y, Lv J, Ding H, Huang J, Huang J, Huang Z, Yang B, Zhang W, Fang X. Improved cure rate of periprosthetic joint infection through targeted antibiotic therapy based on integrated pathogen diagnosis strategy. Front Cell Infect Microbiol 2024; 14:1388385. [PMID: 38836059 PMCID: PMC11148460 DOI: 10.3389/fcimb.2024.1388385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/18/2024] [Indexed: 06/06/2024] Open
Abstract
Objectives This study aimed to determine whether combined of pathogen detection strategies, including specimen acquisition, culture conditions, and molecular diagnostics, can improve treatment outcomes in patients with periprosthetic joint infections (PJI). Methods This retrospective study included suspected PJI cases from three sequential stages at our institution: Stage A (July 2012 to June 2015), Stage B (July 2015 to June 2018), and Stage C (July 2018 to June 2021). Cases were categorized into PJI and aseptic failure (AF) groups based on European Bone and Joint Infection Society (EBJIS) criteria. Utilization of pathogen diagnostic strategies, pathogen detection rates, targeted antibiotic prescription rates, and treatment outcomes were analyzed and compared across the three stages. Results A total of 165 PJI cases and 38 AF cases were included in this study. With the progressive implementation of the three optimization approaches across stages A, B and C, pathogen detection rates exhibited a gradual increase (χ2 = 8.282, P=0.016). Similarly, utilization of targeted antibiotic therapy increased stepwise from 57.1% in Stage A, to 82.3% in Stage B, and to 84% in Stage C (χ2 = 9.515, P=0.009). The 2-year infection control rate exceeded 90% in both stages B and C, surpassing stage A (71.4%) (χ2 = 8.317, P=0.011). Combined application of all three optimized protocols yielded the highest sensitivity of 91.21% for pathogen detection, while retaining higher specificity of 92.11%. Conclusion The utilization of combined pathogen diagnostic strategies in PJI can increase pathogen detection rates, improve targeted antibiotic prescription, reduce the occurrence of antibiotic complications, and achieve better treatment outcomes.
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Affiliation(s)
- Qijin Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Fuan, China
| | - Yongfa Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jianhua Lv
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Haiqi Ding
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiagu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiexin Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Wang B, Wang Q, Li M, Yu J, Jiang F, Hu Y, Guo G, Chen X, Tang J, Han P, Shen H. Diagnostic Role of Metagenomic Next-Generation Sequencing in Tubercular Orthopedic Implant-Associated Infection. Infect Drug Resist 2024; 17:1951-1960. [PMID: 38774035 PMCID: PMC11107837 DOI: 10.2147/idr.s441940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
Objective The diagnosis of tubercular orthopedic implant-associated infection (TB-IAI) is challenging. This study evaluated the value of metagenomic next-generation sequencing (mNGS) for the diagnosis of TB-IAI and developed a standardized diagnostic procedure for TB-IAI. Methods The records of all patients with TB-IAI diagnosed and treated at our institution between December 2018 and September 2022 were retrospectively reviewed. Patient demographic characteristics, medical history, laboratory test, microbial culture, histopathology, and mNGS results, and time to diagnosis were recorded. The diagnostic efficiency of mNGS for TB-IAI was assessed by comparing the results and diagnostic time with that of other diagnostic modalities. Results Ten patients were included in the analysis, including eight with prosthetic joint infections and two with fracture-related infections. The mNGS positivity rate was 100% (10/10), which was higher than that of TB-antibody (11%, 1/9), real-time quantitative polymerase chain reaction (22%, 2/9), T-SPOT.TB (25%, 2/8), purified protein derivative (50%, 4/8), microbial culture (50%, 5/10), and histopathology (20%, 2/10). mNGS shortened the time to diagnosis of TB-IAI. A standardized diagnostic procedure for TB-IAI was developed based on the findings. Conclusion mNGS is useful for the diagnosis of TB-IAI. mNGS is recommended in cases where it is difficult to identify a pathogen using routine diagnostic tests. The standardized diagnostic procedure might improve TB-IAI diagnosis. Importance TB-IAI is a rare infection, which occurs after orthopedic surgery and hard to diagnose microbiologically. mNGS is a new detection technique not yet discussed in current literature as a means for TB-IAI diagnostics. Here we describe a cohort of patients with TB-IAI diagnosed by mNGS show high efficiency of mNGS for detection of this pathology and present a clinical algorithm supplementing conventional methods for TB-IAI assessment.
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Affiliation(s)
- Boyong Wang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Qiaojie Wang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Mingzhang Li
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Jinlong Yu
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Feng Jiang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Yujie Hu
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Geyong Guo
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Jin Tang
- Clinical Laboratory, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Pei Han
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Hao Shen
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
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Huang H, Shi J, Zheng M, Su S, Chen W, Ming J, Ren T, Qu D. Pathogen detection in suspected spinal infection: metagenomic next-generation sequencing versus culture. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2023; 32:4220-4228. [PMID: 37237239 DOI: 10.1007/s00586-023-07707-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 05/28/2023]
Abstract
PURPOSE The aim is to compare the pathogen detection performance of metagenomic next-generation sequencing (mNGS) and the culturing of percutaneous needle biopsy samples obtained from an individual with a suspected spinal infection. METHODS A retrospective study of 141 individuals with a suspected spinal infection was conducted, and mNGS was performed. The microbial spectra and detection performance between mNGS and the culturing-based method were compared, and the effects of antibiotic intervention and biopsy on the detection performance were assessed. RESULTS The microorganisms isolated most commonly via the culturing-based method were Mycobacterium tuberculosis (n = 21), followed by Staphylococcus epidermidis (n = 13). The most common microorganisms detected via mNGS were Mycobacterium tuberculosis complex (MTBC) (n = 39), followed by Staphylococcus aureus (n = 15). The difference in the type of detected microorganisms between culturing and mNGS was observed only in Mycobacterium (P = 0.001). mNGS helped identify potential pathogens in 80.9% of cases, which was significantly higher than the positivity rate of 59.6% observed for the culturing-based method (P < 0.001). Moreover, mNGS had a sensitivity of 85.7% (95% CI, 78.4% to 91.3%), a specificity of 86.7% (95% CI, 59.5% to 98.3%), and sensitivity gains of 35% (85.7% vs. 50.8%; P < 0.001) during culturing, while no differences were observed in the specificity (86.7% vs. 93.3%; P = 0.543). In addition, antibiotic interventions significantly lowered the positivity rate of the culturing-based method (66.0% vs. 45.5%, P = 0.021) but had no effects on the results of mNGS (82.5% vs. 77.3%, P = 0.467). CONCLUSION The use of mNGS could result in a higher detection rate compared to that observed with the culturing-based method in an individual with spinal infection and is particularly valuable for evaluating the effects of a mycobacterial infection or previous antibiotic intervention.
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Affiliation(s)
- Haihong Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiawei Shi
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Minghui Zheng
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Orthopaedic Surgery, Zengcheng Branch of Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shenghui Su
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weidong Chen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing Ming
- Department of Anesthesiology, Nan Fang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Tao Ren
- Department of Orthopaedic Surgery, Zengcheng Branch of Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongbin Qu
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Department of Orthopaedic Surgery, Zengcheng Branch of Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Zhang K, Bai YZ, Liu C, Liu SS, Lu XX, Yang RG. Composition of pathogenic microorganism in chronic osteomyelitis based on metagenomic sequencing and its application value in etiological diagnosis. BMC Microbiol 2023; 23:313. [PMID: 37891467 PMCID: PMC10612345 DOI: 10.1186/s12866-023-03046-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Traditionally, conventional microbiological culture methods have been used to detect pathogenic microorganisms in chronic osteomyelitis. However, these methods have been found to have a low detection rate, complicating the precise guidance of infection treatment. This study employed metagenomic next-generation sequencing (mNGS) to detect these microorganisms in chronic osteomyelitis with three main objectives: 1). Gain a deeper understanding of the composition of pathogenic microorganisms in chronic osteomyelitis. 2). Compare the microbial detection rates between mNGS and the standard culture methods used in laboratories to enhance the effectiveness of the traditional culture methods. 3). Explore the potential of mNGS in etiological diagnosis. METHODS Fifty clinically confirmed intraoperative bone tissue samples of chronic osteomyelitis from January 2021 to December 2021 were collected and subjected to mNGS and microbiological testing, respectively. The orthopaedic surgeon combined clinical manifestations and related examinations to determine the causative pathogens. RESULTS The culture method obtained 29 aerobic and parthenogenic anaerobic bacteria, 3 specific anaerobic bacteria, and 1 yeast-like fungus. Thirty-six aerobic and parthenogenic anaerobic bacteria, 11 specific anaerobic bacteria, and 1 yeast-like fungus were obtained by mNGS, and 2 Mycobacterium tuberculosis(MTB) strains were detected. However, there was no significant difference in the overall positive detection rate between mNGS and the culture method (P = 0.07), and the two were not statistically significant in detecting aerobic and partly anaerobic bacteria (P = 0.625). But, mNGS was significantly superior to culture in detecting anaerobic bacteria and Mycobacterium tuberculosis (P<0.05). CONCLUSIONS The mNGS method has enhanced our understanding of the distribution of pathogenic microorganisms in chronic osteomyelitis. Traditional culture methods help isolate and cultivate aerobic and facultative anaerobic bacteria, and fungi, and are also utilized for antibacterial drug sensitivity tests. However, mNGS has shown superior capabilities in detecting anaerobic bacteria, MTB, and mixed infection bacteria. This finding offers invaluable guidance for improving laboratory microbial culture and detection conditions. Hence, mNGS should be judiciously used for chronic osteomyelitis, and PCR can be implemented for certain difficult-to-culture microorganisms, such as MTB.
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Affiliation(s)
- Kang Zhang
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China
| | - Yu-Zhe Bai
- Department of Tissue Repair and Regeneration, The First Medical Center of PLA General Hospital, Beijing, China
| | - Chang Liu
- Clinical Laboratory of Tsinghua University Hospital, Beijing, China
| | - Shan-Shan Liu
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China
| | - Xin-Xin Lu
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China.
| | - Run-Gong Yang
- Department of Tissue Repair and Regeneration, The First Medical Center of PLA General Hospital, Beijing, China
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Li Z, Yuan Z, Cao H, Huan D, Qiu Y, Xia T, Shen J. A case report on Mycobacterium houstonense infection after total hip arthroplasty. BMC Infect Dis 2023; 23:722. [PMID: 37880617 PMCID: PMC10598912 DOI: 10.1186/s12879-023-08705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Mycobacterium houstonense is a category of rapidly growing mycobacteria that is gram-positive, acid-fast, polycrystalline, and non-spore-forming. There have been few reports of human infection caused by Mycobacterium houstonense worldwide. CASE PRESENTATION We present a case of chronic periprosthetic joint infection caused by Mycobacterium houstonense in an elderly female patient. The patient developed signs of infection after undergoing total hip arthroplasty. Despite receiving antibiotic treatment and revision surgery, the signs of infection recurred repeatedly. Multiple bacterial cultures during the treatment period were negative. Later, we identified the pathogenic bacteria Mycobacterium houstonense through mNGS testing, isolated the bacteria from the ultrasonically centrifuged fluid of the prosthesis and obtained drug sensitivity results. Finally, we performed a revision surgery and treated the patient with moxifloxacin and clindamycin. After treatment, the patient did not show signs of infection recurrence during 24 months of follow-up. CONCLUSION Through a relevant literature search, we believe that Mycobacterium houstonense may show higher sensitivity to amikacin and quinolone antibiotics. Additionally, clarifying occult infection sources through methods such as gene testing will improve the diagnosis and treatment of periprosthetic joint infection.
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Affiliation(s)
- ZhiPeng Li
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - ZhaoFeng Yuan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - HuiLing Cao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - DaWei Huan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - Yue Qiu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - TianWei Xia
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - JiRong Shen
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China.
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Rao Z, Wang Z, Tang M, Zhang K. Optimal Perioperative Antimicrobial Management Strategies of Kidney Transplant Recipients Guided by Metagenomic Next-Generation Sequencing of Deceased Donors' Microbiology Samples. Infect Drug Resist 2023; 16:6473-6486. [PMID: 37795207 PMCID: PMC10547004 DOI: 10.2147/idr.s427656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
Background There is no consensus on the optimal use of perioperative antibiotics prophylaxis after kidney transplantation, but there is a common trend to limit the duration of antibiotic use worldwide. Metagenomic next-generation sequencing (mNGS) has emerged as a novel technology for pathogen detection in clinical practice due to its noninvasive, rapid, precise and high susceptibility to detect infectious pathogens. However, data are lacking on whether mNGS analyses could be used to detect pathogens and guide anti-infection regimens in kidney transplant donors and recipients. Methods We conducted a retrospective study to review all clinic data of mNGS and traditional laboratory methods (TMs) for pathogen detection in kidney transplant recipients and their corresponding deceased donors from August 1, 2021 to October 30, 2022 in our center. Results A total of 57 donors and 112 of their corresponding recipients were included. The antimicrobial strategy mainly depended on mNGS results combined with traditional pathogen culture and clinical conditions. The percentages of positive pathogen detected by mNGS in blood, urine, bronchoalveolar lavage fluid (BALF) and preservation fluids (PFs) were 50.9% (29/57), 35.1% (20/57), 84.2% (48/57) and 54.4% (31/57) respectively, and were 24.6% (14/57), 15.8% (9/57), 57.9% (33/57) and 14.1% (8/57) respectively when using TMs. mNGS could detected all of pathogens which were detected by TMs. However, samples with negative TMs testing can be additionally detected as positive by mNGS (15/43 in blood, 11/48 in urine, 15/24 in BALF and 23/49 in PFs). Drug resistance genes were detected in 9 donors by mNGS,which were consistent with 6 donors by TMs. There was only one case of donor-derived infection in this study. Conclusion This study showed that it is effective to combine mNGS with traditional pathogen detection methods and clinical features to develop optimal perioperative antimicrobial management strategies for deceased donor kidney transplantation.
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Affiliation(s)
- Zhengsheng Rao
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Zhiling Wang
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Ming Tang
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Keqin Zhang
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
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Huang C, Huang Y, Wang Z, Lin Y, Li Y, Chen Y, Chen X, Zhang C, Li W, Zhang W, Fang X, Huang Z. Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis. Front Microbiol 2023; 14:1181348. [PMID: 37275128 PMCID: PMC10232910 DOI: 10.3389/fmicb.2023.1181348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Objectives Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI. Methods PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared. Results Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260). Conclusions tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate. Highlights 298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.
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Affiliation(s)
- Changyu Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ying Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ziwen Wang
- Fujian Medical University, Fuzhou, China
| | - Yiming Lin
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaoqing Chen
- Department of Orthopedic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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He M, Arthur Vithran DT, Pan L, Zeng H, Yang G, Lu B, Zhang F. An update on recent progress of the epidemiology, etiology, diagnosis, and treatment of acute septic arthritis: a review. Front Cell Infect Microbiol 2023; 13:1193645. [PMID: 37249986 PMCID: PMC10214960 DOI: 10.3389/fcimb.2023.1193645] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Acute septic arthritis is on the rise among all patients. Acute septic arthritis must be extensively assessed, identified, and treated to prevent fatal consequences. Antimicrobial therapy administered intravenously has long been considered the gold standard for treating acute osteoarticular infections. According to clinical research, parenteral antibiotics for a few days, followed by oral antibiotics, are safe and effective for treating infections without complications. This article focuses on bringing physicians up-to-date on the most recent findings and discussions about the epidemiology, etiology, diagnosis, and treatment of acute septic arthritis. In recent years, the emergence of antibiotic-resistant, particularly aggressive bacterial species has highlighted the need for more research to enhance treatment approaches and develop innovative diagnosis methods and drugs that might combat better in all patients. This article aims to furnish radiologists, orthopaedic surgeons, and other medical practitioners with contemporary insights on the subject matter and foster collaborative efforts to improve patient outcomes. This review represents the initial comprehensive update encompassing patients across all age groups.
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Affiliation(s)
- Miao He
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Djandan Tadum Arthur Vithran
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linyuan Pan
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haijin Zeng
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guang Yang
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bangbao Lu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fangjie Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Emergency Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Fang B, Lai J, Liu Y, Yu TT, Yu X, Li X, Dong L, Zhang X, Yang W, Yan Q, Sun L, Liu LL. Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019. Front Microbiol 2023; 14:1153728. [PMID: 37007506 PMCID: PMC10060807 DOI: 10.3389/fmicb.2023.1153728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
ObjectivesThis study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).MethodsIn total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.ResultsWe assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.ConclusionThe sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.
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Affiliation(s)
- Bin Fang
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Juan Lai
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Tian-tian Yu
- School of Public Health, Department of Nutritional Hygiene and Toxicology, Wuhan University of Science and Technology, Wuhan, China
| | - Xiao Yu
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Xiang Li
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Lijun Dong
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xin Zhang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Wei Yang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
- *Correspondence: Lei Sun,
| | - Lin-lin Liu
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
- Lin-lin Liu,
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Diagnostic Role of mNGS in Polymicrobial Periprosthetic Joint Infection. J Clin Med 2023; 12:jcm12051838. [PMID: 36902625 PMCID: PMC10003677 DOI: 10.3390/jcm12051838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/02/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVES The purpose of this study was to explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of polymicrobial periprosthetic joint infection (PJI). METHODS Patients with complete data who underwent surgery at our hospital between July 2017 and January 2021 for suspected periprosthetic joint infection (PJI), according to the 2018 ICE diagnostic criteria, were enrolled, and all patients underwent microbial culture and mNGS detection, which were performed on the BGISEQ-500 platform. Microbial cultures were performed on two samples of synovial fluid, six samples of tissue, and two samples of prosthetic sonicate fluid for each patient. The mNGS was performed on 10 tissues, 64 synovial fluid samples, and 17 prosthetic sonicate fluid samples. The results of mNGS testing were based on the interpretation of mNGS results in the previous literature and the assertions of microbiologists and orthopedic surgeons. The diagnostic efficacy of mNGS in polymicrobial PJI was assessed by comparing the results of conventional microbial cultures and mNGS. RESULTS A total of 91 patients were finally enrolled in this study. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of PJI were 71.0%, 95.4%, and 76.9%, respectively. The sensitivity, specificity, and accuracy of mNGS for the diagnosis of PJI were 91.3%, 86.3%, and 90.1%, respectively. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of polymicrobial PJI were 57.1%, 100%, and 91.3%, respectively. mNGS had a sensitivity, specificity, and accuracy of 85.7%, 60.0%, and 65.2%, respectively, for the diagnosis of polymicrobial PJI. CONCLUSIONS mNGS can improve the diagnosis efficiency of polymicrobial PJI, and the combination of culture and mNGS is a promising method to diagnose polymicrobial PJI.
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Wang L, Li S, Qin J, Tang T, Hong J, Tung TH, Xu C, Yu S, Qian J. Clinical Diagnosis Application of Metagenomic Next-Generation Sequencing of Plasma in Suspected Sepsis. Infect Drug Resist 2023; 16:891-901. [PMID: 36820080 PMCID: PMC9938705 DOI: 10.2147/idr.s395700] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
Purpose We analyzed the clinical concordance of mNGS test results from blood samples and improved the clinical efficiency of mNGS in the diagnosis of suspected sepsis pathogens. Patients and Methods In this study, 99 samples of suspected blood flow infection were included for plasma mNGS, and the correlation between mNGS results and blood culture results, serum inflammatory indices, clinical symptoms and antibiotic treatment was analyzed, as well as the comparison with the detection rate of BALF pathogens, as well as the classification of different pathogens in the mNGS results were analyzed. Results The mNGS pathogen detection rate was higher than that of traditional blood culture (83.02% vs 35.82%). The rate of the mNGS results being consistent with the clinical diagnosis was also higher than that of traditional blood culture (58.49% vs 20.75%). This study shows that bacteria and fungi are the main pathogens in sepsis, and viral sepsis is very rare. In this study, 32% of sepsis patients were secondary to pneumonia. Compared with the pathogen detection rate using alveolar lavage fluid, the detection rate from plasma mNGS was 62.5%. Samples were also easy to sample, noninvasive, and more convenient for clinical application. Conclusion This study shows that compared with blood culture, the detection rate of mNGS pathogen that meets the diagnosis of sepsis is higher. We need a combination of multiple indicators to monitor the early diagnosis and treatment of sepsis.
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Affiliation(s)
- Lisha Wang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Shixiao Li
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiajia Qin
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tianbin Tang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiawen Hong
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People’s Republic of China
| | - Chunyan Xu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Sufei Yu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China,Correspondence: Sufei Yu; Jiao Qian, Email ;
| | - Jiao Qian
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
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Zhang B, Chen X, Yao X, Li M, Li Z, Liu B, Liu S, Liu Z, Huo J, Han Y. The diagnostic value of blood metagenomic next-generation sequencing in patients with acute hematogenous osteomyelitis. Front Cell Infect Microbiol 2023; 13:1106097. [PMID: 36779189 PMCID: PMC9911542 DOI: 10.3389/fcimb.2023.1106097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Aims This study aims to evaluate the diagnostic value of blood metagenomic next-generation sequencing (mNGS) in detecting pathogens from patients clinically diagnosed as acute hematogenous osteomyelitis (AHO). Methods This retrospective study enrolled 66 patients with AHO. The test results of mNGS and bacterial culture on different samples, including blood and puncture fluid samples, from patients with AHO were compared to explore the diagnostic value of blood mNGS. Besides, this study also explored the efficacy of blood mNGS in decision making for antibiotic administration and analyzed the factors associated with the positive result of blood mNGS. Results The most common causative pathogens were Staphylococcus and Streptococcus. The sensitivity of blood mNGS (77.3%) was higher than that of blood culture (42.4%) (P<0.001), while the turnaround time of blood mNGS (2.1 ± 0.4 d) is much less than that of blood culture (6.0 ± 2.1 d) (P<0.001). Besides, the sensitivity of blood mNGS tests (77.3%) was slightly lower than that of puncture fluid mNGS (89.4%). Furthermore, detection comparison at pathogen level unravels that blood mNGS might be suitable for diagnosing AHO caused by common pathogens, while puncture fluid mNGS could be considered as preferred examination in diagnosing AHO caused by uncommon pathogens. Finally, three independent factors associated with the true positive result of blood mNGS in patients with AHO were identified, including Gram-positive pathogens (OR=24.4, 95% CI = 1.4-421.0 for Staphylococcus; OR=14.9, 95%CI= 1.6-136.1 for other Gram-positive bacteria), body temperature at sampling time (OR=8.2, 95% CI = 0.6-107.3 for body temperature of >38.5°C; OR=17.2, 95% CI = 2.0-149.1 for patients who were chilling), and no use of antibiotics before sampling (OR=8.9, 95% CI =1.4-59.0). Conclusion This is the first report on evaluating and emphasizing the importance of blood mNGS in diagnosing AHO. Blood sample might be an alternative sample for puncture fluid for mNGS, and its extensive application in diagnosing AHO could be expected.
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Affiliation(s)
- Bingshi Zhang
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Xiao Chen
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Xiaowei Yao
- Department of Orthopedics, The Chest Hospital of Hebei Province, Shijizhuang, Hebei, China
| | - Mengnan Li
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Zhijie Li
- Orthopedics Department, Affiliated Hospital of Hebei Engineering University, Handan, Hebei, China
| | - Bo Liu
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Sikai Liu
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Zeming Liu
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Jia Huo
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Yongtai Han
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China,*Correspondence: Yongtai Han,
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Cai Y, Ding H, Chen X, Chen Y, Huang C, Zhang C, Huang Z, Huang Y, Li W, Zhang W, Fang X. Optimization and standardization of mNGS-based procedures for the diagnosis of Mycoplasma periprosthetic joint infection: A novel diagnostic strategy for rare bacterial periprosthetic joint infection. Front Cell Infect Microbiol 2023; 13:1089919. [PMID: 36936762 PMCID: PMC10014592 DOI: 10.3389/fcimb.2023.1089919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/07/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI. Methods In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR). Results The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases. Conclusion The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI.
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Affiliation(s)
- Yuanqing Cai
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Haiqi Ding
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaoqing Chen
- Department of Orthopedics, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yang Chen
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Changyu Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Chaofan Zhang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Zida Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Ying Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenbo Li
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenming Zhang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Wenming Zhang, ; Xinyu Fang,
| | - Xinyu Fang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Wenming Zhang, ; Xinyu Fang,
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Li Y, Yao XW, Tang L, Dong WJ, Lan TL, Fan J, Liu FS, Qin SB. Diagnostic efficiency of metagenomic next-generation sequencing for suspected spinal tuberculosis in China: A multicenter prospective study. Front Microbiol 2022; 13:1018938. [PMID: 36569091 PMCID: PMC9768024 DOI: 10.3389/fmicb.2022.1018938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Background The pathogens of suspected spinal tuberculosis (TB) include TB and non-TB bacteria. A rapid and effective diagnostic method that can detect TB and non-TB pathogens simultaneously remains lacking. Here, we used metagenomic next-generation sequencing (mNGS) to detect the pathogens in patients with suspected spinal TB. Methods The enrolled patients with suspected spinal TB were regrouped three times into patients with spinal infection and controls, patients with spinal TB and controls, and patients with non-TB spinal infection and controls. We tested the three groups separately by using mNGS and conventional detection methods. Results Ultimately, 100 patients were included in this study. Pathogens were detected in 82 patients. Among the 82 patients, 37 had TB and 45 were infected with other bacteria. In patients with spinal infection, the sensitivity of the mNGS assay was higher than that of culture and pathological examination (p < 0.001, p < 0.001). The specificity of the mNGS assay was not statistically different from that of culture and pathological examination (p = 1.000, p = 1.000). In patients with spinal TB, no statistical difference was found between the sensitivity of the mNGS assay and that of Xpert and T-SPOT.TB (p = 1.000, p = 0.430). The sensitivity of the mNGS assay was higher than that of MGIT 960 culture and pathological examination (p < 0.001, p = 0.006). The specificities of the mNGS assay, Xpert, MGIT 960 culture, and pathological examination were all 100%. The specificity of T-SPOT.TB (78.3%) was lower than that of the mNGS assay (100%; p < 0.001). In patients with non-TB spinal infection, the sensitivity of the mNGS assay was higher than that of bacterial culture and pathological examination (p < 0.001, p < 0.001). The specificity of the mNGS assay was not statistically different from that of bacterial culture and pathological examination (p = 1.000, p = 1.000). Conclusion Data presented here demonstrated that mNGS can detect TB and non-TB bacteria simultaneously, with high sensitivity, specificity and short detection time. Compared with conventional detection methods, mNGS is a more rapid and effective diagnostic tool for suspected spinal TB.
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Affiliation(s)
- Yuan Li
- Department of Orthopedics, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xiao-Wei Yao
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Liang Tang
- Department of Orthopedics, Tianjin Haihe Hospital, Tianjin, China
| | - Wei-Jie Dong
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Ting-Long Lan
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Jun Fan
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Feng-Sheng Liu
- Department of Orthopedics, Tianjin Haihe Hospital, Tianjin, China
| | - Shi-Bing Qin
- Department of Orthopedics, Beijing Chest Hospital, Capital Medical University, Beijing, China
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Zhang C, Lin Y, Huang C, Huang Z, Fang X, Bai G, Zhang Z, Li W, Zhang W. Metagenomic next-generation sequencing assists the diagnosis treatment of fungal osteoarticular infections. Front Cell Infect Microbiol 2022; 12:1072539. [PMID: 36506031 PMCID: PMC9726756 DOI: 10.3389/fcimb.2022.1072539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Background Fungal osteoarticular infection (FOI) is not commonly seen in clinical practice but proposes a great challenge to orthopedic surgeons. In this study, we aimed to investigate the risk factors, the clinical features, and surgical outcomes of FOI in our institution. Specifically, we aimed to explore the role of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of FOI. Methods All the patients who were diagnosed and managed with FOI in our institution from January 2007 to December 2020 were retrospectively reviewed, including primary fungal implant-related infection, primary fungal osteomyelitis or arthritis, and fungal infections secondary to bacterial osteomyelitis or implant-related bacterial infections. The potential risk factors and the clinical and surgical features were analyzed. The pathogen data were compared between culture and the mNGS test. Results A total of 25 patients were included, namely, 12 primary implant-related infections, 7 primary fungal osteomyelitis or arthritis, and 6 fungal infections secondary to bacterial osteomyelitis or implant-related bacterial infections. Most cases had undergone multiple surgeries or long-term antibiotic treatment. Diagnosis was mainly based on microbial culture and the mNGS test. Optimization of culture methods and the use of mNGS assisted the diagnosis. Specifically, mNGS was performed in 12 patients, 5 of whom were culture-negative. In the remaining seven cases, mNGS demonstrated the same results as culture. Management of FOI was complicated as most patients required multiple surgeries followed by long-term antifungal treatment. In selected cases, antifungal-impregnated cement spacer retention can be an optional choice. The overall success rate was 100% (25/25) for our cohort. Conclusion We concluded that patients with comorbidities and a history of multiple surgeries or long-term antibiotics are under higher risk for FOI. Use of mNGS assists the diagnosis and treatment of FOI. Surgery combined with long-term antifungal treatment achieved satisfactory outcomes. In selected cases, antifungal-impregnated cement spacer retention can be an optional treatment choice.
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Affiliation(s)
- Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yunzhi Lin
- Department of Stomatology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Stomatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Changyu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Guochang Bai
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zeyu Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,*Correspondence: Wenming Zhang,
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17
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Yamamoto H, Fukushima Y, Ikeda Y, Suda T, Goto M, Isogai J, Hashimoto T, Takahashi T, Ogino H. Decisive diagnostic clue for infectious abdominal aortic aneurysm caused by Arthrobacter russicus in a diabetic elderly woman with renal dysfunction: A case report and literature review. Front Cardiovasc Med 2022; 9:1007213. [PMID: 36386385 PMCID: PMC9650533 DOI: 10.3389/fcvm.2022.1007213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/26/2022] [Indexed: 12/05/2022] Open
Abstract
Infectious aortic aneurysm (IAA) can be a rare but potentially fatal sequela of infectious inflammatory disease of the aortic wall with a high incidence of rupture. The definitive diagnosis is based on vascular imaging of the aneurysm using contrast-enhanced computed tomography (CE-CT) and identification of the causative microorganism from positive blood cultures (BCs). However, IAA remains extremely difficult to diagnose and treat in patients with prior antimicrobial treatment or with renal dysfunction. Here we describe a case of an 85-year-old woman with IAA caused by Arthrobacter russicus presenting with abdominal pain and fever that was initially diagnosed as a presumptive urinary tract infection and treated with empiric antimicrobial therapy. However, persistent abdominal pain with increased serological inflammation necessitated further evaluation. Unenhanced multimodality imaging considering the renal dysfunction revealed infectious aortitis of the infrarenal abdominal aorta, together with the initial culture results, leading to the tentative diagnosis of Klebsiella pneumoniae aortitis. Thereafter, serial monitoring with unenhanced magnetic resonance angiography (MRA) using thin-slab maximum intensity projection (TS-MIP) revealed acute aortic expansion strongly suggestive of a pseudoaneurysm that was successfully treated with early surgical repair under adequate infection control. Despite negative Gram staining and tissue culture results for the excised aortic wall, a definitive diagnosis of IAA secondary to A. russicus rather than K. pneumoniae was finally made by confirming the histologic findings consistent with IAA and the identification of A. russicus 16S rRNA on the resected aortic wall. The patient also developed a vascular graft infection during the postoperative course that required long-term systemic antimicrobial therapy. This case highlights the value of unenhanced MRA in the early detection of IAA in patients with renal dysfunction and the importance of a molecular diagnosis for identifying the causative microorganism in cases of culture- or tissue-negative IAA.
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Affiliation(s)
- Hiroyuki Yamamoto
- Department of Cardiovascular Medicine, Narita-Tomisato Tokushukai Hospital, Chiba, Japan
- *Correspondence: Hiroyuki Yamamoto,
| | - Yasuto Fukushima
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Omura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Yoshihiko Ikeda
- Department of Pathology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Tomoyuki Suda
- Department of Surgery, Narita-Tomisato Tokushukai Hospital, Chiba, Japan
- Department of General Surgery, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Mieko Goto
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Omura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Jun Isogai
- Department of Radiology, Asahi General Hospital, Asahi, Japan
| | - Toru Hashimoto
- Department of Cardiovascular Medicine, Narita-Tomisato Tokushukai Hospital, Chiba, Japan
| | - Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Omura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Hidemitsu Ogino
- Department of Surgery, Narita-Tomisato Tokushukai Hospital, Chiba, Japan
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18
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Zhang Y, Chen J, Yi X, Chen Z, Yao T, Tang Z, Zang G, Cao X, Lian X, Chen X. Evaluation of the metagenomic next-generation sequencing performance in pathogenic detection in patients with spinal infection. Front Cell Infect Microbiol 2022; 12:967584. [PMID: 36389162 PMCID: PMC9646980 DOI: 10.3389/fcimb.2022.967584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/03/2022] [Indexed: 12/01/2023] Open
Abstract
Spinal infection is a rarely occurred pathology, whose diagnosis remains a major challenge due to the low sensitivity of culturing techniques. Metagenomic next-generation sequencing (mNGS) is a novel approach to identify the pathogenic organisms in infectious diseases. In this study, mNGS technology was adopted for pathogenic detection in spinal infection from the tissue and pus samples. Additionally, the diagnostic performance of mNGS for spinal infection was evaluated, by comparing it with that of the conventional microbial culture, with the histopathological results as the gold standard. Overall, 56 samples from 38 patients were enrolled for mNGS testing, and 69 samples were included for microbial culture. 30 patients (78.95%) were identified to be positive by the mNGS method, which was higher than that of microbial culture (17, 44.74%). The sensitivity and specificity of mNGS with pus samples were 84.2% and 100.0%, respectively, which outperformed those of microbial culture (42.1% and 100.0%). The pathogen identification results were applied to medication guidance, and all 38 patients experienced favorable outcomes at three months, followed-up post-treatment, without any adverse effects. These findings proved that mNGS was superior to microbial culture in pathogenic identification of the spinal infection, thereby showing great promise in guiding drug administration and improving clinical outcomes.
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Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jinmei Chen
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaoli Yi
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Zhiheng Chen
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Ting Yao
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Zhenghao Tang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Guoqing Zang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xuejie Cao
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Xiaofeng Lian
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
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19
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Xu L, Zhou Z, Wang Y, Song C, Tan H. Improved accuracy of etiological diagnosis of spinal infection by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2022; 12:929701. [PMID: 36275025 PMCID: PMC9585211 DOI: 10.3389/fcimb.2022.929701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
Currently, the use of metagenomic next-generation sequencing (mNGS), a new approach to identify organisms in infectious diseases, is rarely reported in the diagnosis of spinal infection. This study aimed to evaluate the potential value of mNGS in etiological diagnosis of spinal infection. In this retrospective study, the clinical data of patients with suspected spinal infection were collected by electronic medical records. Specimens obtained from each patient were tested via mNGS assay and other conventional microbiological tests (CMTs). The sensitivity and specificity of mNGS and CMTs were calculated using the final clinical diagnosis as the golden standard. In total, 108 patients were eligible for the study, with the mean length of stay of 42.8 days. Regarding the overall identification of pathogens, mNGS exhibited a better performance than CMTs, and several nontuberculous mycobacteria, fungi, and bacteria were newly discovered. In the diagnosis of spinal infection, the sensitivity, specificity, and area under the curve of mNGS were 90.72%, 81.82%, and 0.89, respectively, which were all higher than 52.17%, 56.25%, and 0.72 of the CMTs. At hospital discharge, the C-reactive protein, erythrocyte sedimentation rate, and white blood cell count of patients significantly decreased compared with hospitalization (all p < 0.05), and 88.89% showed good outcomes. These findings may suggest that mNGS has a better diagnostic accuracy in pathogenic identification of patients with suspected spinal infection, and patients treated with NGS-guided antimicrobial therapy mostly seem to have good outcomes.
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Affiliation(s)
- Liang Xu
- Department of Spinal Infection, Shandong Public Health Clinical Center, Jinan, China
| | - Zheng Zhou
- Katharine Hsu International Research Institute of Infectious Disease, Shandong Public Health Clinical Center, Jinan, China
| | - Yao Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
- Department of Medicine, Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Hongdong Tan
- Department of Spinal Infection, Shandong Public Health Clinical Center, Jinan, China
- *Correspondence: Hongdong Tan,
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20
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Fang X, Cai Y, Chen X, Huang C, Lin Y, Huang Z, Zhang C, Huang Y, Li W, Zhang W. The role of metagenomic next-generation sequencing in the pathogen detection of invasive osteoarticular infection. Int J Infect Dis 2022; 122:996-1001. [PMID: 35908720 DOI: 10.1016/j.ijid.2022.07.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVE This study aimed to analyzed the pathogenic bacteria spectrum in invasive and primary osteoarticular infection (IOI and POI), and compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and microbial culture in IOI and POI. METHODS The suspected POI and IOI cases from 2008 to 2021 were included. The diagnosis of POI or IOI were made by at least two orthopaedic surgeons, two infectious diseases specialist and one senior microbiologist. Demographic characteristics, microbial culture results and so on were recorded. The pathogenic bacteria spectrum in IOI and POI were analyzed and the ability of mNGS and microbial culture in pathogen detection in IOI and POI were compared. RESULTS There were 63 POI cases and 92 cases, the common pathogen in POI and IOI were both Staphylococcus aureus. There are more cases with negative microbial culture results and multiple infections in IOI, and many cases were caused by rare and fastidious bacteria. The introduction of the mNGS could significantly increase the pathogen detection rate to 92.39% in IOI, which was 8.69% higher than that of microbial culture (P=0.007), while the improvement in POI was limited to about 2%. CONCLUSIONS mNGS was an ideal tool for IOI pathogen detection.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Yuanqing Cai
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Xiaoqing Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China; Department of Orthopaedic Surgery, Quanzhou First Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
| | - Changyu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Yiming Lin
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Ying Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
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21
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Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units. Microbiol Spectr 2022; 10:e0074622. [PMID: 35861525 PMCID: PMC9430677 DOI: 10.1128/spectrum.00746-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of metagenomic next-generation sequencing (mNGS) was evaluated and compared with that of conventional culture testing in patients with sepsis. Prospective blood and bronchoalveolar lavage fluid (BALF) samples from 50 patients with sepsis were tested using cultures (bacterial, fungal, and viral) and mNGS of microbial DNA (blood and BALF) and RNA (BALF). mNGS had higher detection rates than blood culture (88.0% versus 26.0%, P < 0.001) and BALF culture (92.0% versus 76.0%, P = 0.054). RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. The number of multiple detections per specimen was higher in BALF (92.0%) than in blood (78.0%) samples, and the highest number of pathogens detected in a single specimen was 32. Among blood samples, compared to cultures, mNGS detected significantly more bacteria (P < 0.001), fungi (P = 0.012), and viruses (P < 0.001), whereas BALF mNGS had a higher detection rate for bacteria (P < 0.001) and viruses (P < 0.001). The percentage of mNGS-positive samples was significantly higher than that of culture-positive samples for several Gram-negative bacteria, some Gram-positive bacteria, and viruses, but not fungi. Mycobacteria had a higher detection rate by culture than by mNGS, but the difference was not significant due to the small sample size. The positive and negative agreements with 95% confidence intervals of mNGS and culture were 62.0% (50.4 to 72.7) and 96.8% (96.5 to 97.1), respectively. mNGS offers a sensitive diagnostic method for patients with sepsis and is promising for the detection of multipathogen infections. Clinical correlation is advised to interpret mNGS data due to the lack of unified diagnostic criteria. IMPORTANCE Delays in effective antimicrobial therapy have resulted in decreased survival rates among patients with sepsis. However, current culture-based diagnostic methods have low sensitivity because of concurrent antibiotic exposure and fastidious and atypical causative organisms. Among patients with sepsis, we showed that mNGS methods had higher positive rates than culture methods, especially for bacteria, viruses, and multipathogen infections, which are difficult to culture and detect in patients treated with antibiotics. RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. mNGS also showed a high negative percent agreement with cultures. However, the interpretation of mNGS data should be combined with clinical data and conventional methods considering the lack of unified diagnostic criteria.
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22
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Drobish I, Ramchandar N, Raabe V, Pong A, Bradley J, Cannavino C. Pediatric Osteoarticular Infections Caused by Mycobacteria Tuberculosis Complex: A 26-Year Review of Cases in San Diego, CA. Pediatr Infect Dis J 2022; 41:361-367. [PMID: 34974478 DOI: 10.1097/inf.0000000000003447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Osteoarticular infections (OAIs) account for 10%-20% of extrapulmonary Mycobacteria tuberculosis (MTB) complex infections in children and 1%-2% of all pediatric tuberculosis infections. Treatment regimens and durations typically mirror recommendations for other types of extrapulmonary MTB, but there are significant variations in practice, with some experts suggesting a treatment course of 12 months or longer. METHODS We conducted a retrospective review of children diagnosed with MTB complex OAI and cared for between December 31, 1992, and December 31, 2018, at a tertiary care pediatric hospital near the United States-Mexico border. RESULTS We identified 21 children with MTB complex OAI during the study period. Concurrent pulmonary disease (9.5%), meningitis (9.5%), and intra-abdominal involvement (14.3%) were all observed. MTB complex was identified by culture from operative samples in 15/21 children (71.4%); 8/15 (53.3%) cultures were positive for Mycobacterium bovis. Open bone biopsy was the most common procedure for procurement of a tissue sample and had the highest culture yield. The median duration of antimicrobial therapy was 52 weeks (interquartile range, 46-58). Successful completion of therapy was documented in 15 children (71.4%). Nine children (42.9%) experienced long-term sequelae related to their infection. CONCLUSION Among the 21 children with MTB complex OAI assessed, 8 of 15 (53.3%) children with a positive tissue culture had M. bovis, representing a higher percentage than in previous reports and potentially reflecting its presence in unpasteurized dairy products in the California-Baja region. Bone biopsy produced the highest culture yield in this study. Given the rarity of this disease, multicenter collaborative studies are needed to improve our understanding of the presentation and management of pediatric MTB complex OAI.
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Affiliation(s)
- Ian Drobish
- From the University of California, San Diego, California
| | | | - Vanessa Raabe
- New York University Grossman School of Medicine, New York
| | - Alice Pong
- From the University of California, San Diego, California
- Rady Children's Hospital San Diego, San Diego, California
| | - John Bradley
- From the University of California, San Diego, California
- Rady Children's Hospital San Diego, San Diego, California
| | - Christopher Cannavino
- From the University of California, San Diego, California
- Rady Children's Hospital San Diego, San Diego, California
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23
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Zhang XQ, Lei Y, Tan XL, Guo L, Huang XB, Yang FX, Yu H, Liu XS, Wang YP, Lu S, Pan LA. Optimization of Early Antimicrobial Strategies for Lung Transplant Recipients Based on Metagenomic Next-Generation Sequencing. Front Microbiol 2022; 13:839698. [PMID: 35401490 PMCID: PMC8989060 DOI: 10.3389/fmicb.2022.839698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
The management of perioperative antibiotic options after lung transplantation varies widely around the world, but there is a common trend to limit antibiotic use duration. Metagenomic next-generation sequencing (mNGS) has become a hot spot in clinical pathogen detection due to its precise, rapid, and wide detection spectrum of pathogens. Thus, we defined a new antibiotic regimen adjustment strategy in the very early stage (within 7 days) after lung transplantation mainly depending on mNGS reports combined with clinical conditions to reduce the use of antibiotics. To verify the clinical effect of the strategy, we carried out this research. Thirty patients who underwent lung transplantation were finally included, whose information including etiology, antibiotic adjustment, and the effect of our strategy was recorded. Lung transplant recipients in this study were prescribed with initial antibiotic regimen immediately after surgery; their antibiotic regimens were adjusted according to the strategy. According to our study, the entire effectiveness of the strategy was 90.0% (27/30). Besides, a total of 86 samples containing donor lung tissue, recipient lung tissue, and bronchoalveolar lavage fluid (BALF) were obtained in this study; they were all sent to mNGS test, while BALF was also sent to pathogen culture. Their results showed that the positive rate of BALF samples was higher (86.67%) than that of donor’s lung tissue (20.0%) or recipient’s lung tissue (13.33%) by mNGS test, indicating BALF samples are more valuable than other clinical samples from early postoperative period to guide the early adjustment of antibiotics after lung transplantation. It is effective for mNGS combined with traditional methods and clinical situations to optimize antibiotic regimens in lung transplantation recipients within 7 days after surgery.
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Affiliation(s)
- Xiao-qin Zhang
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Yu Lei
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Xiao-li Tan
- Genoxor Medical Science and Technology Inc., Taizhou, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Xiao-bo Huang
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Fu-xun Yang
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Hua Yu
- Department of Microbiology Laboratory, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Xiao-shu Liu
- Department of Pulmonary and Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Yi-ping Wang
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
- *Correspondence: Yi-ping Wang,
| | - Sen Lu
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
- Sen Lu,
| | - Ling-ai Pan
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
- Ling-ai Pan,
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24
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Maamari J, Tande A, Diehn F, Tai DBG, Berbari E. Diagnosis of vertebral osteomyelitis. J Bone Jt Infect 2022; 7:23-32. [PMID: 35136714 PMCID: PMC8814828 DOI: 10.5194/jbji-7-23-2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Native vertebral osteomyelitis (NVO) is a potentially fatal infection which
has seen a gradual increase in its incidence over the past decades. The
infection is insidious, presenting with symptoms of back pain. Fever is
present in about 60 % of patients. Prompt diagnosis of NVO is important to
prevent the development of complications. Numerous laboratory and imaging
tools can be deployed to accurately establish the diagnosis. Imaging
techniques such as magnetic resonance, nuclear imaging, and computed
tomography are essential in diagnosing NVO but can also be useful in
image-guided biopsies. Laboratory tools include routine blood tests,
inflammatory markers, and routine culture techniques of aspirated specimens.
Recent advances in molecular techniques can assist in identifying offending
pathogen(s). In this review, we detail the arsenal of techniques that can be
utilized to reach a diagnosis of NVO.
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Affiliation(s)
- Julian Maamari
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Aaron J. Tande
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Felix Diehn
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | | | - Elie F. Berbari
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
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25
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Xing XW, Yu SF, Zhang JT, Tan RS, Ma YB, Tian X, Wang RF, Yao GE, Cui F, Gui QP, Yu SY. Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Cerebral Aspergillosis. Front Microbiol 2022; 12:787863. [PMID: 35003020 PMCID: PMC8740169 DOI: 10.3389/fmicb.2021.787863] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose: Cerebral aspergillosis (CA) is a rare but often fatal, difficult-to-diagnose, opportunistic infection. The utility of metagenomic next-generation sequencing (mNGS) for diagnosis of CA is unclear. We evaluated the usefulness of mNGS of the cerebrospinal fluid (CSF) for the diagnosis of CA. Methods: This prospective study involved seven consecutive patients with confirmed CA in whom CSF mNGS was performed. Serum (1→3)-β-D-glucan and galactomannan levels were determined, and histopathological examination and mNGS of the CSF were conducted. CSF specimens from three non-infected patients were used as positive controls. Results: mNGS of the CSF was positive in six of the seven confirmed CA cases (85.71% sensitivity). In the cryptococcal meningitis group (control), mNGS of the CSF was positive for Aspergillus in two patients (84.62% specificity). The positive likelihood ratio, negative likelihood ratio, and Youden's index of mNGS for CA in the CSF were 5.565, 0.169, and 0.7, respectively. Among the six mNGS-positive cases, more than two Aspergillus species were found in four (4/6, 66.67%). In the positive controls, the addition of one A. fumigatus spore yielded a standardised species-specific read number (SDSSRN) of 25.45 by mNGS; the detection rate would be 0.98 if SDSSRN was 2. Conclusion: mNGS facilitates the diagnosis of CA and may reduce the need for cerebral biopsy in patients with suspected CA. Trial Registration Number: Chinese Clinical Trial Registry, ChiCTR1800020442.
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Affiliation(s)
- Xiao-Wei Xing
- Department of Neurology, Hainan Hospital of Chinese PLA General Hospital, Sanya, China
| | - Su-Fei Yu
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China
| | - Jia-Tang Zhang
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing, China.,Chinese PLA Medical School, Beijing, China
| | | | - Yu-Bao Ma
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xia Tian
- Department of Pathology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Rong-Fei Wang
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Guo-En Yao
- Department of Neurology, Fourth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fang Cui
- Department of Neurology, Hainan Hospital of Chinese PLA General Hospital, Sanya, China
| | - Qiu-Ping Gui
- Department of Pathology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Sheng-Yuan Yu
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing, China.,Chinese PLA Medical School, Beijing, China
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26
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Castañeda-Mogollón D, Kamaliddin C, Oberding L, Liu Y, Mohon AN, Faridi RM, Khan F, Pillai DR. A metagenomics workflow for SARS-CoV-2 identification, co-pathogen detection, and overall diversity. J Clin Virol 2021; 145:105025. [PMID: 34775144 PMCID: PMC8564975 DOI: 10.1016/j.jcv.2021.105025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 12/24/2022]
Abstract
An unbiased metagenomics approach to virus identification can be essential in the initial phase of a pandemic. Better molecular surveillance strategies are needed for the detection of SARS-CoV-2 variants of concern and potential co-pathogens triggering respiratory symptoms. Here, a metagenomics workflow was developed to identify the metagenome diversity by SARS-CoV-2 diagnosis (npositive = 65; nnegative = 60), symptomatology status (nsymptomatic = 71; nasymptomatic = 54) and anatomical swabbing site (nnasopharyngeal = 96; nthroat = 29) in 125 individuals. Furthermore, the workflow was able to identify putative respiratory co-pathogens, and the SARS-CoV-2 lineage across 29 samples. The diversity analysis showed a significant shift in the DNA-metagenome by symptomatology status and anatomical swabbing site. Additionally, metagenomic diversity differed between SARS-CoV-2 infected and uninfected asymptomatic individuals. While 31 co-pathogens were identified in SARS-CoV-2 infected patients, no significant increase in pathogen or associated reads were noted when compared to SARS-CoV-2 negative patients. The Alpha SARS-CoV-2 VOC and 2 variants of interest (Zeta) were successfully identified for the first time using a clinical metagenomics approach. The metagenomics pipeline showed a sensitivity of 86% and a specificity of 72% for the detection of SARS-CoV-2. Clinical metagenomics can be employed to identify SARS-CoV-2 variants and respiratory co-pathogens potentially contributing to COVID-19 symptoms. The overall diversity analysis suggests a complex set of microorganisms with different genomic abundance profiles in SARS-CoV-2 infected patients compared to healthy controls. More studies are needed to correlate severity of COVID-19 disease in relation to potential disbyosis in the upper respiratory tract. A metagenomics approach is particularly useful when novel pandemic pathogens emerge.
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Affiliation(s)
- Daniel Castañeda-Mogollón
- Cumming School of Medicine, Department of Pathology & Laboratory Medicine, the University of Calgary, AB, Canada; Cumming School of Medicine, Department of Microbiology, Immunology, and Infectious Diseases, the University of Calgary, Canada; Calvin, Phoebe & Joan Snyder Institute for Chronic Diseases, the University of Calgary, Calgary, AB, Canada
| | - Claire Kamaliddin
- Cumming School of Medicine, Department of Pathology & Laboratory Medicine, the University of Calgary, AB, Canada; Cumming School of Medicine, Department of Microbiology, Immunology, and Infectious Diseases, the University of Calgary, Canada; Calvin, Phoebe & Joan Snyder Institute for Chronic Diseases, the University of Calgary, Calgary, AB, Canada
| | - Lisa Oberding
- Cumming School of Medicine, Department of Pathology & Laboratory Medicine, the University of Calgary, AB, Canada; Cumming School of Medicine, Department of Microbiology, Immunology, and Infectious Diseases, the University of Calgary, Canada; Calvin, Phoebe & Joan Snyder Institute for Chronic Diseases, the University of Calgary, Calgary, AB, Canada
| | - Yan Liu
- Cumming School of Medicine, Department of Pathology & Laboratory Medicine, the University of Calgary, AB, Canada; Cumming School of Medicine, Department of Microbiology, Immunology, and Infectious Diseases, the University of Calgary, Canada; Calvin, Phoebe & Joan Snyder Institute for Chronic Diseases, the University of Calgary, Calgary, AB, Canada
| | - Abu Naser Mohon
- Cumming School of Medicine, Department of Pathology & Laboratory Medicine, the University of Calgary, AB, Canada; Cumming School of Medicine, Department of Microbiology, Immunology, and Infectious Diseases, the University of Calgary, Canada; Calvin, Phoebe & Joan Snyder Institute for Chronic Diseases, the University of Calgary, Calgary, AB, Canada
| | - Rehan Mujeeb Faridi
- Alberta Precision Laboratories, Diagnostic & Scientific Centre, Calgary, AB, Canada; Hematology Translational Lab, University of Calgary, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, the University of Calgary, Calgary, AB, Canada
| | - Faisal Khan
- Alberta Precision Laboratories, Diagnostic & Scientific Centre, Calgary, AB, Canada; Hematology Translational Lab, University of Calgary, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, the University of Calgary, Calgary, AB, Canada
| | - Dylan R Pillai
- Cumming School of Medicine, Department of Pathology & Laboratory Medicine, the University of Calgary, AB, Canada; Cumming School of Medicine, Department of Microbiology, Immunology, and Infectious Diseases, the University of Calgary, Canada; Calvin, Phoebe & Joan Snyder Institute for Chronic Diseases, the University of Calgary, Calgary, AB, Canada; Alberta Precision Laboratories, Diagnostic & Scientific Centre, Calgary, AB, Canada.
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27
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Cai S, Yang Y, Pan J, Miao Q, Jin W, Ma Y, Zhou C, Gao X, Wang C, Hu B. The clinical value of valve metagenomic next-generation sequencing when applied to the etiological diagnosis of infective endocarditis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1490. [PMID: 34805352 PMCID: PMC8573444 DOI: 10.21037/atm-21-2488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Background Metagenomic next-generation sequencing (mNGS) is widely applied in the etiological diagnosis of infectious diseases. However, the clinical practice of mNGS in infective endocarditis (IE) is relatively less studied. This research aimed to assess the etiological diagnostic value of valve mNGS in IE. Methods We retrospectively analyzed 49 IE patients who underwent cardiac valve surgery in Zhongshan Hospital, Fudan University, Shanghai from 1 June 2018 to 30 November 2020. Among these IE patients, 28 were culture positive and 21 were culture negative. The culture results of the culture-positive IE patients were set as gold standard to assess the sensitivity and specificity of valve mNGS in the etiological diagnosis of IE. We studied the positive detection rate of pathogens by valve mNGS among the culture-negative IE patients. During the same period, we also collected the resected valves of 8 patients with non-infective valvular diseases for mNGS as negative controls. Results The valve mNGS results of the culture-positive IE patients were the exact same as their culture results. Both the sensitivity and specificity of valve mNGS were 100%. The positive detection rate of pathogens by valve mNGS was 100% among the culture-negative IE patients. The stringent mapped reads number of genera (SMRNG), relative abundance of genera, stringent mapped reads number of species (SMRN), relative abundance of species, and coverage rate of valve mNGS results were significantly higher in culture-positive IE participants than in culture-negative IE participants. The valve mNGS results of the 8 participants with non-infective valvular diseases were all negative. Conclusions Valve mNGS is a promising technology for the etiological diagnosis of IE, especially culture-negative IE, and it may be used to guide precise antibiotic treatment after surgery.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ye Yang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunsheng Wang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
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28
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Dong S, Lin Z, Wu S, Cai L. Spondylitis following bloodstream dissemination of Mycobacterium chelonae disseminated in an immunocompetent patient: a case report and literature review. J Int Med Res 2021; 49:3000605211047766. [PMID: 34590879 PMCID: PMC8489759 DOI: 10.1177/03000605211047766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Non-tuberculous mycobacterial spondylitis is a rare spinal infection, especially among patients without acquired immunodeficiency syndrome or other immune impairments. Because of its rarity and non-specific clinical manifestations, diagnosis is often delayed or missed. Here, we present a case of Mycobacterium chelonae spondylitis in an immunocompetent patient and review the relevant literature.
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Affiliation(s)
- Shuangxia Dong
- Department of Respiratory Medicine, The Wenzhou Central Hospital and Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zhou Lin
- Department of Orthopaedic Surgery, The Wenzhou Central Hospital and Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shenghao Wu
- Department of Hematology, The Wenzhou Central Hospital and Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Leyi Cai
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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29
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Ramchandar N, Burns J, Coufal NG, Pennock A, Briggs B, Stinnett R, Bradley J, Arnold J, Liu GY, Pring M, Upasani VV, Rickert K, Dimmock D, Chiu C, Farnaes L, Cannavino C. Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections. Open Forum Infect Dis 2021; 8:ofab346. [PMID: 34322569 PMCID: PMC8314938 DOI: 10.1093/ofid/ofab346] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Osteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children. METHODS This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children's hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon's discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site. RESULTS We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS. CONCLUSIONS In this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.
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Affiliation(s)
- Nanda Ramchandar
- Pediatric Infectious Disease, University of California, San Diego, San Diego, California, USA
| | - Jessica Burns
- Pediatric Orthopedics, University of California, San Diego, San Diego, California, USA
| | - Nicole G Coufal
- Pediatric Critical Care, University of California, San Diego, San Diego, California, USA
| | - Andrew Pennock
- Pediatric Orthopedics, University of California, San Diego, San Diego, California, USA
| | | | | | - John Bradley
- Pediatric Infectious Disease, University of California, San Diego, San Diego, California, USA
| | - John Arnold
- Pediatric Infectious Disease, University of California, San Diego, San Diego, California, USA
| | - George Y Liu
- Pediatric Infectious Disease, University of California, San Diego, San Diego, California, USA
| | - Maya Pring
- Pediatric Orthopedics, University of California, San Diego, San Diego, California, USA
| | - Vidyadhar V Upasani
- Pediatric Orthopedics, University of California, San Diego, San Diego, California, USA
| | - Kathleen Rickert
- Pediatric Orthopedics, University of California, San Diego, San Diego, California, USA
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, California, USA
| | - Charles Chiu
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lauge Farnaes
- Pediatric Infectious Disease, University of California, San Diego, San Diego, California, USA
- IDbyDNA, Salt Lake City, Utah, USA
| | - Christopher Cannavino
- Pediatric Infectious Disease, University of California, San Diego, San Diego, California, USA
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30
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Sun L, Yang Z, Yang F, Wang Z, Li H, Wang H, Sun T. Diagnosis of Mycobacterium tuberculosis Septic Shock in Patients With Anti-synthetase Syndrome Based on Next-Generation Sequencing: A Case Report and Literature Review. Front Med (Lausanne) 2021; 8:675041. [PMID: 34277657 PMCID: PMC8281055 DOI: 10.3389/fmed.2021.675041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/03/2021] [Indexed: 12/27/2022] Open
Abstract
A 51-year-old woman was transferred to the intensive care unit with such symptoms as fever, swollen left knee joint, pain and hypotension. After preliminary evaluation, she was diagnosed as suffering acute suppurative arthritis and septic shock. Then, she was rescued and prescribed to receive treatment with broad-spectrum antibiotics. However, there was no source of infection identified except for the knee joint. The bacterial and fungal cultures of blood samples and articular effusion were shown to be negative, while the results obtained from the next-generation sequencing of blood and articular effusion revealed that Mycobacterium tuberculosis was positive. The patient was then put on five combinations of anti-tuberculosis therapeutic treatment. Nevertheless, despite the active anti-tuberculosis treatment put in place, her general condition still deteriorated progressively. As the level of her bilirubin continued to rise, further treatment was affected, which prompted the change made to the anti-tuberculosis treatment program. Her clinical condition continued to deteriorate, which led to the development of unstable vital signs and the multiple organ dysfunction syndrome. In spite of our best efforts to save her life, the patient still ended up with death.
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Affiliation(s)
- Limin Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziyue Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Wang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongqiang Li
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tongwen Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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31
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Gamie Z, Karthikappallil D, Gamie E, Stamiris S, Kenanidis E, Tsiridis E. Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections. Expert Rev Mol Diagn 2021; 22:603-624. [PMID: 33641572 DOI: 10.1080/14737159.2021.1894929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Prosthetic joint infections (PJIs) can be challenging to eradicate and have high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been linked to a greater rate of reoperation. AREAS COVERED There has been increasing investigation of the use of next-generation sequencing (NGS) technology such as metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction (PCR) has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJIs when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further toward routine clinical practice. EXPERT OPINION Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJIs are diagnosed, managed, and drastically improve outcomes from this currently devastating complication.
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Affiliation(s)
- Zakareya Gamie
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK; Genomic Medicine - St George's, University of London, Cranmer Terrace, Tooting, London, SW17 0RE; King's College London, Strand, London
| | - Dileep Karthikappallil
- Department of Trauma and Orthopedics, East Cheshire NHS Trust, Macclesfield District General Hospital, Victoria Road, Macclesfield, Cheshire, SK10 3BL, UK
| | - Emane Gamie
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; MBiol, BSc Biological Sciences, University of Leeds Alumni, UK
| | - Stavros Stamiris
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eustathios Kenanidis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eleftherios Tsiridis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
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